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Merge branch 'master' into kh_2526_Add_Operation_Section_to_Conformance_Statements_resource_section

This commit is contained in:
Kevin Hartmann 2021-04-26 16:53:19 -04:00
parent bb9c7a43e7 0246e7dd0e
commit 2f126a8d9f
309 changed files with 9307 additions and 5205 deletions
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1
.editorconfig
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@ -31,6 +31,7 @@ charset = utf-8
indent_style = tab
tab_width = 3
indent_size = 3
continuation_indent_size=3
ij_java_align_consecutive_assignments = false
ij_java_align_consecutive_variable_declarations = false
ij_java_align_group_field_declarations = false

2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/BaseRuntimeDeclaredChildDefinition.java
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@ -22,6 +22,7 @@ package ca.uhn.fhir.context;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.util.ParametersUtil;
import ca.uhn.fhir.util.ValidateUtil;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
@ -60,7 +61,7 @@ public abstract class BaseRuntimeDeclaredChildDefinition extends BaseRuntimeChil
myElementName = theElementName;
if (theDescriptionAnnotation != null) {
myShortDefinition = theDescriptionAnnotation.shortDefinition();
myFormalDefinition = theDescriptionAnnotation.formalDefinition();
myFormalDefinition = ParametersUtil.extractDescription(theDescriptionAnnotation);
} else {
myShortDefinition = null;
myFormalDefinition = null;

38
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/phonetic/NumericEncoder.java Normal file
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@ -0,0 +1,38 @@
package ca.uhn.fhir.context.phonetic;
/*-
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import com.google.common.base.CharMatcher;
// Useful for numerical identifiers like phone numbers, address parts etc.
// This should not be used where decimals are important. A new "quantity encoder" should be added to handle cases like that.
public class NumericEncoder implements IPhoneticEncoder {
@Override
public String name() {
return "NUMERIC";
}
@Override
public String encode(String theString) {
// Remove everything but the numbers
return CharMatcher.inRange('0', '9').retainFrom(theString);
}
}

3
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/phonetic/PhoneticEncoderEnum.java
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@ -39,7 +39,8 @@ public enum PhoneticEncoderEnum {
METAPHONE(new ApacheEncoder("METAPHONE", new Metaphone())),
NYSIIS(new ApacheEncoder("NYSIIS", new Nysiis())),
REFINED_SOUNDEX(new ApacheEncoder("REFINED_SOUNDEX", new RefinedSoundex())),
SOUNDEX(new ApacheEncoder("SOUNDEX", new Soundex()));
SOUNDEX(new ApacheEncoder("SOUNDEX", new Soundex())),
NUMERIC(new NumericEncoder());
private final IPhoneticEncoder myPhoneticEncoder;

18
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/api/annotation/Description.java
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@ -30,9 +30,16 @@ import java.lang.annotation.Target;
* a search parameter definition in order to provide documentation for that item.
*/
@Retention(RetentionPolicy.RUNTIME)
@Target(value= {ElementType.FIELD, ElementType.TYPE, ElementType.PARAMETER, ElementType.METHOD})
@Target(value = {ElementType.FIELD, ElementType.TYPE, ElementType.PARAMETER, ElementType.METHOD})
public @interface Description {
/**
* A description of this method or parameter
*
* @since 5.4.0
*/
String value() default "";
/**
* Optional short name for this child
*/
@ -40,7 +47,16 @@ public @interface Description {
/**
* Optional formal definition for this child
*
* @deprecated Use {@link #value()} instead. Deprecated in 5.4.0.
*/
@Deprecated
String formalDefinition() default "";
/**
* May be used to supply example values for this
*
* @since 5.4.0
*/
String[] example() default {};
}

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/AddTags.java
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@ -78,4 +78,13 @@ public @interface AddTags {
*/
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Create.java
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@ -47,4 +47,13 @@ public @interface Create {
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

11
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Delete.java
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@ -48,4 +48,15 @@ public @interface Delete {
*/
// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/DeleteTags.java
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@ -74,4 +74,14 @@ public @interface DeleteTags {
*/
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/History.java
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@ -81,4 +81,14 @@ public @interface History {
*/
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Operation.java
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@ -132,7 +132,10 @@ public @interface Operation {
/**
* If this is set to <code>true</code>, this method will be a <b>global operation</b>
* meaning that it applies to all resource types
* meaning that it applies to all resource types. Operations with this flag set should be
* placed in Plain Providers (i.e. they don't need to be placed in a resource-type-specific
* <code>IResourceProvider</code> instance) and should have a parameter annotated with
* {@link IdParam}.
*/
boolean global() default false;

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/OperationParam.java
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@ -39,7 +39,7 @@ public @interface OperationParam {
/**
* Value for {@link OperationParam#max()} indicating no maximum
*/
final int MAX_UNLIMITED = -1;
int MAX_UNLIMITED = -1;
/**
@ -57,7 +57,7 @@ public @interface OperationParam {
*
* @since 1.5
*/
final int MAX_DEFAULT = -2;
int MAX_DEFAULT = -2;
/**
* The name of the parameter

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Patch.java
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@ -50,4 +50,13 @@ public @interface Patch {
// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

11
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Search.java
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@ -78,6 +78,16 @@ public @interface Search {
// NB: Read, Search (maybe others) share this annotation method, so update the javadocs everywhere
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
/**
* In a REST server, should this method be invoked even if it does not have method parameters
* which correspond to all of the URL parameters passed in by the client (default is <code>false</code>).
@ -91,4 +101,5 @@ public @interface Search {
* </p>
*/
boolean allowUnknownParams() default false;
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Update.java
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@ -49,4 +49,14 @@ public @interface Update {
// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
Class<? extends IResource> type() default IResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
* <p>
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
}

10
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/Validate.java
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@ -53,6 +53,16 @@ public @interface Validate {
// NB: Read, Search (maybe others) share this annotation, so update the javadocs everywhere
Class<? extends IBaseResource> type() default IBaseResource.class;
/**
* This method allows the return type for this method to be specified in a
* non-type-specific way, using the text name of the resource, e.g. "Patient".
*
* This attribute should be populate, or {@link #type()} should be, but not both.
*
* @since 5.4.0
*/
String typeName() default "";
/**
* Validation mode parameter annotation for the validation mode parameter (only supported
* in FHIR DSTU2+). Parameter must be of type {@link ValidationModeEnum}.

53
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleBuilder.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.primitive.IdDt;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
@ -156,7 +157,8 @@ public class BundleBuilder {
// Bundle.entry.request.url
IPrimitiveType<?> url = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
url.setValueAsString(theResource.getIdElement().toUnqualifiedVersionless().getValue());
String resourceType = myContext.getResourceType(theResource);
url.setValueAsString(theResource.getIdElement().toUnqualifiedVersionless().withResourceType(resourceType).getValue());
myEntryRequestUrlChild.getMutator().setValue(request, url);
// Bundle.entry.request.url
@ -193,6 +195,45 @@ public class BundleBuilder {
return new CreateBuilder(request);
}
/**
* Adds an entry containing a delete (DELETE) request.
* Also sets the Bundle.type value to "transaction" if it is not already set.
*
* Note that the resource is only used to extract its ID and type, and the body of the resource is not included in the entry,
*
* @param theResource The resource to delete.
*/
public void addTransactionDeleteEntry(IBaseResource theResource) {
String resourceType = myContext.getResourceType(theResource);
String idPart = theResource.getIdElement().toUnqualifiedVersionless().getIdPart();
addTransactionDeleteEntry(resourceType, idPart);
}
/**
* Adds an entry containing a delete (DELETE) request.
* Also sets the Bundle.type value to "transaction" if it is not already set.
*
* @param theResourceType The type resource to delete.
* @param theIdPart the ID of the resource to delete.
*/
public void addTransactionDeleteEntry(String theResourceType, String theIdPart) {
setBundleField("type", "transaction");
IBase request = addEntryAndReturnRequest();
IdDt idDt = new IdDt(theIdPart);
// Bundle.entry.request.url
IPrimitiveType<?> url = (IPrimitiveType<?>) myContext.getElementDefinition("uri").newInstance();
url.setValueAsString(idDt.toUnqualifiedVersionless().withResourceType(theResourceType).getValue());
myEntryRequestUrlChild.getMutator().setValue(request, url);
// Bundle.entry.request.method
IPrimitiveType<?> method = (IPrimitiveType<?>) myEntryRequestMethodDef.newInstance(myEntryRequestMethodChild.getInstanceConstructorArguments());
method.setValueAsString("DELETE");
myEntryRequestMethodChild.getMutator().setValue(request, method);
}
/**
* Adds an entry for a Collection bundle type
*/
@ -250,6 +291,16 @@ public class BundleBuilder {
return request;
}
public IBase addEntryAndReturnRequest() {
IBase entry = addEntry();
// Bundle.entry.request
IBase request = myEntryRequestDef.newInstance();
myEntryRequestChild.getMutator().setValue(entry, request);
return request;
}
public IBaseBundle getBundle() {
return myBundle;

47
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ExtensionUtil.java
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@ -36,6 +36,13 @@ import java.util.stream.Collectors;
*/
public class ExtensionUtil {
/**
* Non instantiable
*/
private ExtensionUtil() {
// nothing
}
/**
* Returns an extension with the specified URL creating one if it doesn't exist.
*
@ -46,7 +53,7 @@ public class ExtensionUtil {
*/
public static IBaseExtension<?, ?> getOrCreateExtension(IBase theBase, String theUrl) {
IBaseHasExtensions baseHasExtensions = validateExtensionSupport(theBase);
IBaseExtension extension = getExtensionByUrl(baseHasExtensions, theUrl);
IBaseExtension<?,?> extension = getExtensionByUrl(baseHasExtensions, theUrl);
if (extension == null) {
extension = baseHasExtensions.addExtension();
extension.setUrl(theUrl);
@ -75,13 +82,27 @@ public class ExtensionUtil {
*/
public static IBaseExtension<?, ?> addExtension(IBase theBase, String theUrl) {
IBaseHasExtensions baseHasExtensions = validateExtensionSupport(theBase);
IBaseExtension extension = baseHasExtensions.addExtension();
IBaseExtension<?,?> extension = baseHasExtensions.addExtension();
if (theUrl != null) {
extension.setUrl(theUrl);
}
return extension;
}
/**
* Adds an extension with the specified value
*
* @param theBase The resource to update extension on
* @param theUrl Extension URL
* @param theValueType Type of the value to set in the extension
* @param theValue Extension value
* @param theFhirContext The context containing FHIR resource definitions
*/
public static void addExtension(FhirContext theFhirContext, IBase theBase, String theUrl, String theValueType, Object theValue) {
IBaseExtension<?,?> ext = addExtension(theBase, theUrl);
setExtension(theFhirContext, ext, theValueType, theValue);
}
private static IBaseHasExtensions validateExtensionSupport(IBase theBase) {
if (!(theBase instanceof IBaseHasExtensions)) {
throw new IllegalArgumentException(String.format("Expected instance that supports extensions, but got %s", theBase));
@ -118,7 +139,7 @@ public class ExtensionUtil {
if (!hasExtension(theBase, theExtensionUrl)) {
return false;
}
IBaseDatatype value = getExtensionByUrl((IBaseHasExtensions) theBase, theExtensionUrl).getValue();
IBaseDatatype value = getExtensionByUrl(theBase, theExtensionUrl).getValue();
if (value == null) {
return theExtensionValue == null;
}
@ -133,7 +154,7 @@ public class ExtensionUtil {
* @return Returns the first available extension with the specified URL, or null if such extension doesn't exist
*/
public static IBaseExtension<?, ?> getExtensionByUrl(IBase theBase, String theExtensionUrl) {
Predicate<IBaseExtension> filter;
Predicate<IBaseExtension<?,?>> filter;
if (theExtensionUrl == null) {
filter = (e -> true);
} else {
@ -153,7 +174,7 @@ public class ExtensionUtil {
* @param theFilter Predicate to match the extension against
* @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
*/
public static List<IBaseExtension<?, ?>> getExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
public static List<IBaseExtension<?, ?>> getExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension<?,?>> theFilter) {
return validateExtensionSupport(theBase)
.getExtension()
.stream()
@ -189,7 +210,7 @@ public class ExtensionUtil {
* @param theFilter Defines which extensions should be cleared
* @return Returns all extension that were removed
*/
private static List<IBaseExtension<?, ?>> clearExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension> theFilter) {
private static List<IBaseExtension<?, ?>> clearExtensionsMatchingPredicate(IBase theBase, Predicate<? super IBaseExtension<?,?>> theFilter) {
List<IBaseExtension<?, ?>> retVal = getExtensionsMatchingPredicate(theBase, theFilter);
validateExtensionSupport(theBase)
.getExtension()
@ -205,7 +226,7 @@ public class ExtensionUtil {
* @return Returns all extension with the specified URL, or an empty list if such extensions do not exist
*/
public static List<IBaseExtension<?, ?>> getExtensionsByUrl(IBaseHasExtensions theBase, String theExtensionUrl) {
Predicate<IBaseExtension> urlEqualityPredicate = e -> theExtensionUrl.equals(e.getUrl());
Predicate<IBaseExtension<?,?>> urlEqualityPredicate = e -> theExtensionUrl.equals(e.getUrl());
return getExtensionsMatchingPredicate(theBase, urlEqualityPredicate);
}
@ -216,8 +237,8 @@ public class ExtensionUtil {
* @param theValue The value to set
* @param theFhirContext The context containing FHIR resource definitions
*/
public static void setExtension(FhirContext theFhirContext, IBaseExtension theExtension, String theValue) {
setExtension(theFhirContext, theExtension, "string", (Object) theValue);
public static void setExtension(FhirContext theFhirContext, IBaseExtension<?,?> theExtension, String theValue) {
setExtension(theFhirContext, theExtension, "string", theValue);
}
/**
@ -228,7 +249,7 @@ public class ExtensionUtil {
* @param theValue The value to set
* @param theFhirContext The context containing FHIR resource definitions
*/
public static void setExtension(FhirContext theFhirContext, IBaseExtension theExtension, String theExtensionType, Object theValue) {
public static void setExtension(FhirContext theFhirContext, IBaseExtension<?,?> theExtension, String theExtensionType, Object theValue) {
theExtension.setValue(TerserUtil.newElement(theFhirContext, theExtensionType, theValue));
}
@ -241,7 +262,7 @@ public class ExtensionUtil {
* @param theFhirContext The context containing FHIR resource definitions
*/
public static void setExtensionAsString(FhirContext theFhirContext, IBase theBase, String theUrl, String theValue) {
IBaseExtension ext = getOrCreateExtension(theBase, theUrl);
IBaseExtension<?,?> ext = getOrCreateExtension(theBase, theUrl);
setExtension(theFhirContext, ext, theValue);
}
@ -255,7 +276,7 @@ public class ExtensionUtil {
* @param theFhirContext The context containing FHIR resource definitions
*/
public static void setExtension(FhirContext theFhirContext, IBase theBase, String theUrl, String theValueType, Object theValue) {
IBaseExtension ext = getOrCreateExtension(theBase, theUrl);
IBaseExtension<?,?> ext = getOrCreateExtension(theBase, theUrl);
setExtension(theFhirContext, ext, theValueType, theValue);
}
@ -266,7 +287,7 @@ public class ExtensionUtil {
* @param theRightExtension : Extension to be evaluated #2
* @return Result of the comparison
*/
public static boolean equals(IBaseExtension theLeftExtension, IBaseExtension theRightExtension) {
public static boolean equals(IBaseExtension<?,?> theLeftExtension, IBaseExtension<?,?> theRightExtension) {
return TerserUtil.equals(theLeftExtension, theRightExtension);
}
}

8
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/HapiExtensions.java
View File

@ -116,7 +116,13 @@ public class HapiExtensions {
*/
public static final String ASSOCIATED_GOLDEN_RESOURCE_EXTENSION_URL = "https://hapifhir.org/associated-patient-golden-resource/";
/**
/**
* This extension provides an example value for a parameter value for
* a REST operation (eg for an OperationDefinition)
*/
public static final String EXT_OP_PARAMETER_EXAMPLE_VALUE = "http://hapifhir.io/fhir/StructureDefinition/op-parameter-example-value";
/**
* Non instantiable
*/
private HapiExtensions() {

63
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/ParametersUtil.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.primitive.StringDt;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBase;
@ -34,8 +35,13 @@ import org.hl7.fhir.instance.model.api.IBaseReference;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import javax.annotation.Nullable;
import java.lang.annotation.Annotation;
import java.lang.reflect.AnnotatedElement;
import java.lang.reflect.Method;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
@ -43,6 +49,7 @@ import java.util.function.Function;
import java.util.stream.Collectors;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.isBlank;
/**
* Utilities for dealing with parameters resources in a version indepenedent way
@ -418,4 +425,60 @@ public class ParametersUtil {
.findFirst();
}
@Nullable
public static String extractDescription(AnnotatedElement theType) {
Description description = theType.getAnnotation(Description.class);
if (description != null) {
return extractDescription(description);
} else {
return null;
}
}
@Nullable
public static String extractDescription(Description desc) {
String description = desc.value();
if (isBlank(description)) {
description = desc.formalDefinition();
}
if (isBlank(description)) {
description = desc.shortDefinition();
}
return defaultIfBlank(description, null);
}
@Nullable
public static String extractShortDefinition(AnnotatedElement theType) {
Description description = theType.getAnnotation(Description.class);
if (description != null) {
return defaultIfBlank(description.shortDefinition(), null);
} else {
return null;
}
}
public static String extractDescription(Annotation[] theParameterAnnotations) {
for (Annotation next : theParameterAnnotations) {
if (next instanceof Description) {
return extractDescription((Description)next);
}
}
return null;
}
public static List<String> extractExamples(Annotation[] theParameterAnnotations) {
ArrayList<String> retVal = null;
for (Annotation next : theParameterAnnotations) {
if (next instanceof Description) {
String[] examples = ((Description) next).example();
if (examples.length > 0) {
if (retVal == null) {
retVal = new ArrayList<>();
}
retVal.addAll(Arrays.asList(examples));
}
}
}
return retVal;
}
}

92
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/TerserUtil.java
View File

@ -25,6 +25,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
import ca.uhn.fhir.context.BaseRuntimeElementDefinition;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import org.apache.commons.lang3.tuple.Triple;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
@ -48,9 +49,15 @@ public final class TerserUtil {
private static final String EQUALS_DEEP = "equalsDeep";
/**
* Exclude for id, identifier and meta fields of a resource.
*/
public static final Collection<String> IDS_AND_META_EXCLUDES =
Collections.unmodifiableSet(Stream.of("id", "identifier", "meta").collect(Collectors.toSet()));
/**
* Exclusion predicate for id, identifier, meta fields.
*/
public static final Predicate<String> EXCLUDE_IDS_AND_META = new Predicate<String>() {
@Override
public boolean test(String s) {
@ -58,6 +65,25 @@ public final class TerserUtil {
}
};
/**
* Exclusion predicate for id/identifier, meta and fields with empty values. This ensures that source / target resources,
* empty source fields will not results in erasure of target fields.
*/
public static final Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>> EXCLUDE_IDS_META_AND_EMPTY = new Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>>() {
@Override
public boolean test(Triple<BaseRuntimeChildDefinition, IBase, IBase> theTriple) {
if (!EXCLUDE_IDS_AND_META.test(theTriple.getLeft().getElementName())) {
return false;
}
BaseRuntimeChildDefinition childDefinition = theTriple.getLeft();
boolean isSourceFieldEmpty = childDefinition.getAccessor().getValues(theTriple.getMiddle()).isEmpty();
return !isSourceFieldEmpty;
}
};
/**
* Exclusion predicate for keeping all fields.
*/
public static final Predicate<String> INCLUDE_ALL = new Predicate<String>() {
@Override
public boolean test(String s) {
@ -235,24 +261,35 @@ public final class TerserUtil {
}
/**
* Replaces all fields that test positive by the given inclusion strategy. <code>theTo</code> will contain a copy of the
* Replaces all fields that have matching field names by the given inclusion strategy. <code>theTo</code> will contain a copy of the
* values from <code>theFrom</code> instance.
*
* @param theFhirContext Context holding resource definition
* @param theFrom The resource to merge the fields from
* @param theTo The resource to merge the fields into
* @param inclusionStrategy Inclusion strategy that checks if a given field should be replaced by checking {@link Predicate#test(Object)}
* @param theFhirContext Context holding resource definition
* @param theFrom The resource to merge the fields from
* @param theTo The resource to merge the fields into
* @param theFieldNameInclusion Inclusion strategy that checks if a given field should be replaced
*/
public static void replaceFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<String> inclusionStrategy) {
FhirTerser terser = theFhirContext.newTerser();
public static void replaceFields(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<String> theFieldNameInclusion) {
Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>> predicate
= (t) -> theFieldNameInclusion.test(t.getLeft().getElementName());
replaceFieldsByPredicate(theFhirContext, theFrom, theTo, predicate);
}
/**
* Replaces fields on theTo resource that test positive by the given predicate. <code>theTo</code> will contain a copy of the
* values from <code>theFrom</code> for which predicate tests positive. Please note that composite fields will be replaced fully.
*
* @param theFhirContext Context holding resource definition
* @param theFrom The resource to merge the fields from
* @param theTo The resource to merge the fields into
* @param thePredicate Predicate that checks if a given field should be replaced
*/
public static void replaceFieldsByPredicate(FhirContext theFhirContext, IBaseResource theFrom, IBaseResource theTo, Predicate<Triple<BaseRuntimeChildDefinition, IBase, IBase>> thePredicate) {
RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
for (BaseRuntimeChildDefinition childDefinition : definition.getChildrenAndExtension()) {
if (!inclusionStrategy.test(childDefinition.getElementName())) {
continue;
if (thePredicate.test(Triple.of(childDefinition, theFrom, theTo))) {
replaceField(theFrom, theTo, childDefinition);
}
replaceField(theFrom, theTo, childDefinition);
}
}
@ -277,14 +314,11 @@ public final class TerserUtil {
* @param theTo The resource to replace the field on
*/
public static void replaceField(FhirContext theFhirContext, String theFieldName, IBaseResource theFrom, IBaseResource theTo) {
replaceField(theFhirContext, theFhirContext.newTerser(), theFieldName, theFrom, theTo);
}
/**
* @deprecated Use {@link #replaceField(FhirContext, String, IBaseResource, IBaseResource)} instead
*/
public static void replaceField(FhirContext theFhirContext, FhirTerser theTerser, String theFieldName, IBaseResource theFrom, IBaseResource theTo) {
replaceField(theFrom, theTo, getBaseRuntimeChildDefinition(theFhirContext, theFieldName, theFrom));
RuntimeResourceDefinition definition = theFhirContext.getResourceDefinition(theFrom);
if (definition == null) {
throw new IllegalArgumentException(String.format("Field %s does not exist in %s", theFieldName, theFrom));
}
replaceField(theFrom, theTo, theFhirContext.getResourceDefinition(theFrom).getChildByName(theFieldName));
}
/**
@ -301,7 +335,7 @@ public final class TerserUtil {
/**
* Sets the provided field with the given values. This method will add to the collection of existing field values
* in case of multiple cardinality. Use {@link #clearField(FhirContext, FhirTerser, String, IBaseResource, IBase...)}
* in case of multiple cardinality. Use {@link #clearField(FhirContext, String, IBaseResource)}
* to remove values before setting
*
* @param theFhirContext Context holding resource definition
@ -315,7 +349,7 @@ public final class TerserUtil {
/**
* Sets the provided field with the given values. This method will add to the collection of existing field values
* in case of multiple cardinality. Use {@link #clearField(FhirContext, FhirTerser, String, IBaseResource, IBase...)}
* in case of multiple cardinality. Use {@link #clearField(FhirContext, String, IBaseResource)}
* to remove values before setting
*
* @param theFhirContext Context holding resource definition
@ -370,10 +404,26 @@ public final class TerserUtil {
setFieldByFhirPath(theFhirContext.newTerser(), theFhirPath, theResource, theValue);
}
/**
* Returns field values ant the specified FHIR path from the resource.
*
* @param theFhirContext Context holding resource definition
* @param theFhirPath The FHIR path to get the field from
* @param theResource The resource from which the value should be retrieved
* @return Returns the list of field values at the given FHIR path
*/
public static List<IBase> getFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBase theResource) {
return theFhirContext.newTerser().getValues(theResource, theFhirPath, false, false);
}
/**
* Returns the first available field value at the specified FHIR path from the resource.
*
* @param theFhirContext Context holding resource definition
* @param theFhirPath The FHIR path to get the field from
* @param theResource The resource from which the value should be retrieved
* @return Returns the first available value or null if no values can be retrieved
*/
public static IBase getFirstFieldByFhirPath(FhirContext theFhirContext, String theFhirPath, IBase theResource) {
List<IBase> values = getFieldByFhirPath(theFhirContext, theFhirPath, theResource);
if (values == null || values.isEmpty()) {

6
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java
View File

@ -68,7 +68,11 @@ public enum VersionEnum {
V5_2_0,
V5_2_1,
V5_3_0,
V5_4_0;
V5_3_1,
V5_3_2,
V5_3_3,
V5_4_0,
;
public static VersionEnum latestVersion() {
VersionEnum[] values = VersionEnum.values();

7
hapi-fhir-base/src/main/java/ca/uhn/fhir/validation/SchemaBaseValidator.java
View File

@ -51,6 +51,7 @@ public class SchemaBaseValidator implements IValidatorModule {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SchemaBaseValidator.class);
private static final Set<String> SCHEMA_NAMES;
private static boolean ourJaxp15Supported;
static {
HashSet<String> sn = new HashSet<>();
@ -132,7 +133,9 @@ public class SchemaBaseValidator implements IValidatorModule {
* https://www.owasp.org/index.php/XML_External_Entity_(XXE)_Processing
*/
schemaFactory.setProperty(XMLConstants.ACCESS_EXTERNAL_DTD, "");
ourJaxp15Supported = true;
} catch (SAXNotRecognizedException e) {
ourJaxp15Supported = false;
ourLog.warn("Jaxp 1.5 Support not found.", e);
}
schema = schemaFactory.newSchema(new Source[]{baseSource});
@ -216,4 +219,8 @@ public class SchemaBaseValidator implements IValidatorModule {
}
public static boolean isJaxp15Supported() {
return ourJaxp15Supported;
}
}

4
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -68,8 +68,8 @@ ca.uhn.fhir.validation.ValidationResult.noIssuesDetected=No issues detected duri
# JPA Messages
ca.uhn.fhir.jpa.bulk.svc.BulkDataExportSvcImpl.onlyBinarySelected=Binary resources may not be exported with bulk export
ca.uhn.fhir.jpa.bulk.svc.BulkDataExportSvcImpl.unknownResourceType=Unknown or unsupported resource type: {0}
ca.uhn.fhir.jpa.bulk.export.svc.BulkDataExportSvcImpl.onlyBinarySelected=Binary resources may not be exported with bulk export
ca.uhn.fhir.jpa.bulk.export.svc.BulkDataExportSvcImpl.unknownResourceType=Unknown or unsupported resource type: {0}
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceVersionConstraintFailure=The operation has failed with a version constraint failure. This generally means that two clients/threads were trying to update the same resource at the same time, and this request was chosen as the failing request.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.resourceIndexedCompositeStringUniqueConstraintFailure=The operation has failed with a unique index constraint failure. This probably means that the operation was trying to create/update a resource that would have resulted in a duplicate value for a unique index.
ca.uhn.fhir.jpa.config.HapiFhirHibernateJpaDialect.forcedIdConstraintFailure=The operation has failed with a client-assigned ID constraint failure. This typically means that multiple client threads are trying to create a new resource with the same client-assigned ID at the same time, and this thread was chosen to be rejected.

12
hapi-fhir-base/src/test/java/ca/uhn/fhir/context/phonetic/PhoneticEncoderTest.java
View File

@ -1,14 +1,14 @@
package ca.uhn.fhir.context.phonetic;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.EnumSource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import static org.hamcrest.Matchers.startsWith;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.endsWith;
import static org.hamcrest.Matchers.startsWith;
import static org.junit.jupiter.api.Assertions.assertEquals;
class PhoneticEncoderTest {
private static final Logger ourLog = LoggerFactory.getLogger(PhoneticEncoderTest.class);
@ -23,7 +23,11 @@ class PhoneticEncoderTest {
public void testEncodeAddress(PhoneticEncoderEnum thePhoneticEncoderEnum) {
String encoded = thePhoneticEncoderEnum.getPhoneticEncoder().encode(ADDRESS_LINE);
ourLog.info("{}: {}", thePhoneticEncoderEnum.name(), encoded);
assertThat(encoded, startsWith(NUMBER + " "));
assertThat(encoded, endsWith(" " + SUITE));
if (thePhoneticEncoderEnum == PhoneticEncoderEnum.NUMERIC) {
assertEquals(NUMBER + SUITE, encoded);
} else {
assertThat(encoded, startsWith(NUMBER + " "));
assertThat(encoded, endsWith(" " + SUITE));
}
}
}

1
hapi-fhir-base/src/test/java/ca/uhn/fhir/validation/PlaceholderTest.java
View File

@ -11,5 +11,4 @@ public class PlaceholderTest {
public void testPass() {
// nothing
}
}

9
hapi-fhir-bom/pom.xml
View File

@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -41,6 +41,11 @@
<artifactId>hapi-fhir-server-mdm</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>hapi-fhir-server-openapi</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>${project.groupId}</groupId>
<artifactId>hapi-fhir-validation</artifactId>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

15
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java
View File

@ -31,6 +31,7 @@ import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
@ -70,6 +71,9 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
protected static final String VERBOSE_LOGGING_PARAM = "l";
protected static final String VERBOSE_LOGGING_PARAM_LONGOPT = "logging";
protected static final String VERBOSE_LOGGING_PARAM_DESC = "If specified, verbose logging will be used.";
protected static final int DEFAULT_THREAD_COUNT = 10;
protected static final String THREAD_COUNT = "thread-count";
// TODO: Don't use qualified names for loggers in HAPI CLI.
private static final Logger ourLog = LoggerFactory.getLogger(BaseCommand.class);
protected FhirContext myFhirCtx;
@ -87,6 +91,11 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
addOptionalOption(theOptions, null, BEARER_TOKEN_PARAM_LONGOPT, BEARER_TOKEN_PARAM_NAME, BEARER_TOKEN_PARAM_DESC);
}
protected void addThreadCountOption(Options theOptions) {
addOptionalOption(theOptions, null, THREAD_COUNT, "count", "If specified, this argument specifies the number of worker threads used (default is " + DEFAULT_THREAD_COUNT + ")");
}
protected String promptUser(String thePrompt) throws ParseException {
System.out.print(ansi().bold().fgBrightDefault());
System.out.print(thePrompt);
@ -309,6 +318,12 @@ public abstract class BaseCommand implements Comparable<BaseCommand> {
return getFhirContext().getResourceDefinition("Bundle").getImplementingClass(IBaseBundle.class);
}
protected int getThreadCount(CommandLine theCommandLine) throws ParseException {
Integer parallelismThreadCount = getAndParsePositiveIntegerParam(theCommandLine, THREAD_COUNT);
parallelismThreadCount = ObjectUtils.defaultIfNull(parallelismThreadCount, DEFAULT_THREAD_COUNT);
return parallelismThreadCount.intValue();
}
public abstract String getCommandDescription();
public abstract String getCommandName();

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/OperationMethodBinding.java
View File

@ -30,6 +30,7 @@ import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.FhirTerser;
import ca.uhn.fhir.util.ParametersUtil;
import org.hl7.fhir.instance.model.api.*;
import java.lang.reflect.Method;
@ -64,10 +65,7 @@ public class OperationMethodBinding extends BaseResourceReturningMethodBinding {
Description description = theMethod.getAnnotation(Description.class);
if (description != null) {
myDescription = description.formalDefinition();
if (isBlank(myDescription)) {
myDescription = description.shortDefinition();
}
myDescription = ParametersUtil.extractDescription(description);
}
if (isBlank(myDescription)) {
myDescription = null;

11
hapi-fhir-client/src/main/java/ca/uhn/fhir/rest/client/method/SearchMethodBinding.java
View File

@ -33,6 +33,7 @@ import ca.uhn.fhir.rest.client.impl.BaseHttpClientInvocation;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
@ -59,15 +60,7 @@ public class SearchMethodBinding extends BaseResourceReturningMethodBinding {
this.myQueryName = StringUtils.defaultIfBlank(search.queryName(), null);
this.myCompartmentName = StringUtils.defaultIfBlank(search.compartmentName(), null);
this.myIdParamIndex = ParameterUtil.findIdParameterIndex(theMethod, getContext());
Description desc = theMethod.getAnnotation(Description.class);
if (desc != null) {
if (isNotBlank(desc.formalDefinition())) {
myDescription = StringUtils.defaultIfBlank(desc.formalDefinition(), null);
} else {
myDescription = StringUtils.defaultIfBlank(desc.shortDefinition(), null);
}
}
this.myDescription = ParametersUtil.extractDescription(theMethod);
/*
* Check for parameter combinations and names that are invalid

2
hapi-fhir-converter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

15
hapi-fhir-docs/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -55,6 +55,11 @@
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-openapi</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.dataformat</groupId>
@ -78,13 +83,13 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-subscription</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<scope>compile</scope>
</dependency>
<dependency>
@ -101,7 +106,7 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-testpage-overlay</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<classifier>classes</classifier>
</dependency>
<dependency>
@ -118,7 +123,7 @@
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
</dependencies>
</dependencies>
<build>
<plugins>

73
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/CreateCompositionAndGenerateDocument.java Normal file
View File

@ -0,0 +1,73 @@
package ca.uhn.hapi.fhir.docs;
/*-
* #%L
* HAPI FHIR - Docs
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.client.api.IGenericClient;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Reference;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class CreateCompositionAndGenerateDocument {
private static final Logger ourLog = LoggerFactory.getLogger(CreateCompositionAndGenerateDocument.class);
public static void main(String[] args) {
// START SNIPPET: CreateCompositionAndGenerateDocument
FhirContext ctx = FhirContext.forR4();
IGenericClient client = ctx.newRestfulGenericClient("http://hapi.fhir.org/baseR4");
Patient patient = new Patient();
patient.setId("PATIENT-ABC");
patient.setActive(true);
client.update().resource(patient).execute();
Observation observation = new Observation();
observation.setId("OBSERVATION-ABC");
observation.setSubject(new Reference("Patient/PATIENT-ABC"));
observation.setStatus(Observation.ObservationStatus.FINAL);
client.update().resource(observation).execute();
Composition composition = new Composition();
composition.setId("COMPOSITION-ABC");
composition.setSubject(new Reference("Patient/PATIENT-ABC"));
composition.addSection().setFocus(new Reference("Observation/OBSERVATION-ABC"));
client.update().resource(composition).execute();
Bundle document = client
.operation()
.onInstance("Composition/COMPOSITION-ABC")
.named("$document")
.withNoParameters(Parameters.class)
.returnResourceType(Bundle.class)
.execute();
ourLog.info("Document bundle: {}", ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(document));
// END SNIPPET: CreateCompositionAndGenerateDocument
}
}

19
hapi-fhir-docs/src/main/java/ca/uhn/hapi/fhir/docs/ServletExamples.java
View File

@ -23,6 +23,7 @@ package ca.uhn.hapi.fhir.docs;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.rest.api.PreferHandlingEnum;
import ca.uhn.fhir.rest.openapi.OpenApiInterceptor;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.interceptor.*;
@ -65,6 +66,24 @@ public class ServletExamples {
}
// END SNIPPET: loggingInterceptor
// START SNIPPET: OpenApiInterceptor
@WebServlet(urlPatterns = { "/fhir/*" }, displayName = "FHIR Server")
public class RestfulServerWithOpenApi extends RestfulServer {
@Override
protected void initialize() throws ServletException {
// ... define your resource providers here ...
// Now register the interceptor
OpenApiInterceptor openApiInterceptor = new OpenApiInterceptor();
registerInterceptor(openApiInterceptor);
}
}
// END SNIPPET: OpenApiInterceptor
// START SNIPPET: validatingInterceptor
@WebServlet(urlPatterns = { "/fhir/*" }, displayName = "FHIR Server")
public class ValidatingServerWithLogging extends RestfulServer {

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_1/version.yaml Normal file
View File

@ -0,0 +1,3 @@
---
release-date: "2021-03-11"
codename: "Odyssey"

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_2/version.yaml Normal file
View File

@ -0,0 +1,3 @@
---
release-date: "2021-04-14"
codename: "Odyssey"

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_3_3/version.yaml Normal file
View File

@ -0,0 +1,3 @@
---
release-date: "2021-04-26"
codename: "Odyssey"

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2407-allow-partition-date-for-nonpartitionable.yaml
View File

@ -4,3 +4,4 @@ issue: 2407
title: "When using the JPA server in partitioned mode with a partition interceptor, the interceptor is now called even for
resource types that can not be placed in a non-default partition (e.g. SearchParameter, CodeSystem, etc.). The interceptor
may return null or default in this case, but can include a non-null partition date if needed."
backport: 5.3.1

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2417-avoid-npe-indexing-timing.yaml
View File

@ -3,3 +3,4 @@ type: fix
issue: 2417
title: "A NullPointerException was corrected when indexing resources containing an indexed Period field that
had a start but not an end defined."
backport: 5.3.3

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2515-mdm-survivorship-rules-application.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2515
title: "Fixed issues with application of survivorship rules when matching golden record to a single resource"

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2533-fix-issue-with-reference-resources-not-being-returned-in-search-queries.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: fix
issue: 2533
title: "When issuing a request for a specific Resource and also specifying an _include param,
the referenced resource is not returned when there is only 1 version of the referenced resource available.
When there are more than 1 versions available, the referenced resource is returned in the response bundle."
backport: 5.3.2

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2535-do-not-create-snapshot-for-logical-structuredefinition.yaml Normal file
View File

@ -0,0 +1,6 @@
---
type: fix
issue: 2535
title: "An issue with package installer involving logical StructureDefinition resources was fixed. Package registry will no
longer attempt to generate a snapshot for logical StructureDefinition resources if one is not already provided in the
resource definition."

9
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2543-fix-issue-where-versionned-references-are-not-being-returned-properly.yaml Normal file
View File

@ -0,0 +1,9 @@
---
type: fix
issue: 2543
title: "When issuing a request for a specific Resource and also specifying an _include param,
the proper historical referenced resource is not returned when there are more than 1 versions of the
referenced resource available, after the reference has been changed from the original version 1 to some other version.
When there are more than 1 versions available, and the referring resource had previously referred to version 1
but now refers to version 4, the resource returned in the response bundle is for version 1."
backport: 5.3.2

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2547-mdm-add-numeric-matcher.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 2547
title: "Added new NUMERIC mdm matcher for matching phone numbers. Also added NUMERIC phonetic encoder to support
adding NUMERIC encoded search parameter (e.g. if searching for matching phone numbers is required by mdm candidate searching)."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2556-prevent-bulk-failure-while-partitioned.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2556
title: "Fixed a bug which would cause Bulk Export to fail when run in a partitioned environment."

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2560-openapi-support.yaml Normal file
View File

@ -0,0 +1,5 @@
---
type: add
issue: 2560
title: "A new interceptor called `OpenApiInterceptor` has been added. This interceptor can be registered against FHIR Servers to
automatically add support for OpenAPI / Swagger."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/2571-add-delete-to-bundle-builder.yaml Normal file
View File

@ -0,0 +1,4 @@
---
type: fix
issue: 2571
title: "Added support for deleting resources to BundleBuilder via method `addTransactionDeleteEntry`."

27
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_4_0/changes.yaml Normal file
View File

@ -0,0 +1,27 @@
---
- item:
type: "add"
title: "The version of a few dependencies have been bumped to the latest versions
(dependent HAPI modules listed in brackets):
<ul>
<li>Commons-Lang3 (Core): 3.9 -> 3.12.0</li>
<li>Commons-Text (Core): 1.7 -> 1.9</li>
<li>Commons-Codec (Core): 1.14 -> 1.15</li>
<li>Commons-IO (Core): 2.6 -> 2.8.0</li>
<li>Guava (Core): 30.1-jre -> 30.1.1-jre</li>
<li>Jackson (Core): 2.12.1 -> 2.12.3</li>
<li>Woodstox (Core): 6.2.3 -> 6.2.5</li>
<li>Apache Jena (Core/RDF): 3.16.0 -> 3.17.0</li>
<li>Gson (JPA): 2.8.5 -> 2.8.6</li>
<li>Caffeine (JPA): 2.7.0 -> 3.0.1</li>
<li>Hibernate (JPA): 5.4.26.Final -> 5.4.30.Final</li>
<li>Hibernate Search (JPA): 6.0.0.Final -> 6.0.2.Final</li>
<li>Spring (JPA): 5.3.3 -> 5.3.6</li>
<li>Spring Batch (JPA): 4.2.3.RELEASE -> 4.3.2</li>
<li>Spring Data (JPA): 2.4.2 -> 2.4.7</li>
<li>Commons DBCP2 (JPA): 2.7.0 -> 2.8.0</li>
<li>Thymeleaf (Testpage Overlay): 3.0.11.RELEASE -> 3.0.12.RELEASE</li>
<li>JAnsi (CLI): 2.1.1 -> 2.3.2</li>
<li>JArchivelib (CLI): 1.0.0 -> 1.1.0</li>
</ul>
"

10
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/client/examples.md
View File

@ -161,3 +161,13 @@ This following example shows how to load all pages of a bundle by fetching each
```java
{{snippet:classpath:/ca/uhn/hapi/fhir/docs/BundleFetcher.java|loadAll}}
```
# Create Composition and Generate Document
This example shows how to generate a Composition resource with two linked resources, then apply the server `$document` operation to generate a document based on this composition.
```java
{{snippet:classpath:/ca/uhn/hapi/fhir/docs/CreateCompositionAndGenerateDocument.java|CreateCompositionAndGenerateDocument}}
```

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties
View File

@ -47,6 +47,7 @@ page.server_plain.web_testpage_overlay=Web Testpage Overlay
page.server_plain.multitenancy=Multitenancy
page.server_plain.jax_rs=JAX-RS Support
page.server_plain.customizing_the_capabilitystatement=Customizing the CapabilityStatement
page.server_plain.openapi=OpenAPI / Swagger
section.server_jpa.title=JPA Server
page.server_jpa.introduction=Introduction

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/interceptors/built_in_server_interceptors.md
View File

@ -196,6 +196,11 @@ Some security audit tools require that servers return an HTTP 405 if an unsuppor
* [BanUnsupportedHttpMethodsInterceptor JavaDoc](/apidocs/hapi-fhir-server/ca/uhn/fhir/rest/server/interceptor/BanUnsupportedHttpMethodsInterceptor.html)
* [BanUnsupportedHttpMethodsInterceptor Source](https://github.com/hapifhir/hapi-fhir/blob/master/hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BanUnsupportedHttpMethodsInterceptor.java)
# Server: OpenAPI / Swagger Support
An interceptor can be registered against your server that enables support for OpenAPI (aka Swagger) automatically. See [OpenAPI](/docs/server_plain/openapi.html) for more information.
# Subscription: Subscription Debug Log Interceptor
When using Subscriptions, the debug log interceptor can be used to add a number of additional lines to the server logs showing the internals of the subscription processing pipeline.

12
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_mdm/mdm_rules.md
View File

@ -292,10 +292,10 @@ The following algorithms are currently supported:
<td>Gail = Gael, Gail != Gale, Thomas != Tom</td>
</tr>
<tr>
<td>CAVERPHONE1</td>
<td>CAVERPHONE2</td>
<td>matcher</td>
<td>
<a href="https://commons.apache.org/proper/commons-codec/apidocs/org/apache/commons/codec/language/Caverphone1.html">Apache Caverphone1</a>
<a href="https://commons.apache.org/proper/commons-codec/apidocs/org/apache/commons/codec/language/Caverphone2.html">Apache Caverphone2</a>
</td>
<td>Gail = Gael, Gail = Gale, Thomas != Tom</td>
</tr>
@ -379,6 +379,14 @@ The following algorithms are currently supported:
</td>
<td>2019-12,Month = 2019-12-19,Day</td>
</tr>
<tr>
<td>NUMERIC</td>
<td>matcher</td>
<td>
Remove all non-numeric characters from the string before comparing.
</td>
<td>4169671111 = (416) 967-1111</td>
</tr>
<tr>
<td>NAME_ANY_ORDER</td>
<td>matcher</td>

39
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/openapi.md Normal file
View File

@ -0,0 +1,39 @@
# OpenAPI / Swagger Support
In HAPI FHIR, support for OpenAPI (aka Swagger) is supported via the [OpenApiInterceptor](/hapi-fhir/apidocs/hapi-fhir-server-openapi/ca/uhn/fhir/rest/openapi/OpenApiInterceptor.html).
Note that this interceptor supports servers using the RestfulServer (aka HAPI FHIR Plain Server and JPA Server), and does not currently support JAX-RS servers.
When this interceptor is registered against the server, it performs the following 3 tasks:
### System Functionality
* OpenAPI 3.0 Documentation will be served at `[baseUrl]/api-docs`. This documentation is generated by the interceptor using information from the server's CapabilityStatement as well as from its automatically generated OperationDefinitions.
### User Functionality
* Anytime a user using a browser navigates to the Base URL of the server, they will be automatically redirected to `[baseUrl]/swagger-ui/`
* A customized version of the [Swagger UI](https://swagger.io/tools/swagger-ui/) tool will be served at `[baseUrl]/swagger-ui/`
# Enabling OpenAPI
The HAPI FHIR OpenAPI functionality is supplied in a dedicated module called `hapi-fhir-server-openapi`. To enable this functionality you must first include this module in your project. For example, Maven users should include the following dependency:
```xml
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-openapi</artifactId>
<version>VERSION</version>
</dependency>
```
You then simply have to register the interceptor against your RestfulServer instance.
```java
{{snippet:classpath:/ca/uhn/hapi/fhir/docs/ServletExamples.java|OpenApiInterceptor}}
```
# Demonstration
See the HAPI FHIR Test Server for a demonstration of HAPI FHIR OpenAPI functionality: http://hapi.fhir.org/baseR4/swagger-ui/

7
hapi-fhir-jacoco/pom.xml
View File

@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -36,6 +36,11 @@
<artifactId>hapi-fhir-server-mdm</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-openapi</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-client</artifactId>

2
hapi-fhir-jaxrsserver-base/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-example/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-api/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

12
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirSystemDao.java
View File

@ -67,6 +67,18 @@ public interface IFhirSystemDao<T, MT> extends IDao {
*/
IBaseBundle processMessage(RequestDetails theRequestDetails, IBaseBundle theMessage);
/**
* Executes a FHIR transaction using a new database transaction. This method must
* not be called from within a DB transaction.
*/
T transaction(RequestDetails theRequestDetails, T theResources);
/**
* Executes a FHIR transaction nested inside the current database transaction.
* This form of the transaction processor can handle write operations only (no reads)
*/
default T transactionNested(RequestDetails theRequestDetails, T theResources) {
throw new UnsupportedOperationException();
}
}

11
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>5.4.0-PRE5-SNAPSHOT</version>
<version>5.4.0-PRE8-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
@ -577,7 +577,14 @@
<scope>test</scope>
</dependency>
<dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-server-openapi</artifactId>
<version>${project.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
</dependency>

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java
View File

@ -20,17 +20,20 @@ package ca.uhn.fhir.jpa.batch;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.job.BulkImportJobConfig;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@Configuration
//When you define a new batch job, add it here.
@Import({
CommonBatchJobConfig.class,
BulkExportJobConfig.class
CommonBatchJobConfig.class,
BulkExportJobConfig.class,
BulkImportJobConfig.class
})
public class BatchJobsConfig {
public static final String BULK_IMPORT_JOB_NAME = "bulkImportJob";
public static final String BULK_EXPORT_JOB_NAME = "bulkExportJob";
public static final String GROUP_BULK_EXPORT_JOB_NAME = "groupBulkExportJob";
public static final String PATIENT_BULK_EXPORT_JOB_NAME = "patientBulkExportJob";

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/processors/GoldenResourceAnnotatingProcessor.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.util.ExtensionUtil;
import ca.uhn.fhir.util.HapiExtensions;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/api/BulkDataExportOptions.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/api/BulkDataExportOptions.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.api;
package ca.uhn.fhir.jpa.bulk.export.api;
/*-
* #%L

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/api/IBulkDataExportSvc.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/api/IBulkDataExportSvc.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.api;
package ca.uhn.fhir.jpa.bulk.export.api;
/*-
* #%L
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.api;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.transaction.Transactional;
@ -50,7 +50,7 @@ public interface IBulkDataExportSvc {
class JobInfo {
private String myJobId;
private BulkJobStatusEnum myStatus;
private BulkExportJobStatusEnum myStatus;
private List<FileEntry> myFiles;
private String myRequest;
private Date myStatusTime;
@ -90,11 +90,11 @@ public interface IBulkDataExportSvc {
}
public BulkJobStatusEnum getStatus() {
public BulkExportJobStatusEnum getStatus() {
return myStatus;
}
public JobInfo setStatus(BulkJobStatusEnum theStatus) {
public JobInfo setStatus(BulkExportJobStatusEnum theStatus) {
myStatus = theStatus;
return this;
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BaseBulkItemReader.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BaseBulkItemReader.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -30,7 +30,6 @@ import ca.uhn.fhir.jpa.dao.ISearchBuilder;
import ca.uhn.fhir.jpa.dao.SearchBuilderFactory;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.jpa.entity.Search;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -102,7 +101,7 @@ public abstract class BaseBulkItemReader implements ItemReader<List<ResourcePers
myPidIterator = getResourcePidIterator();
}
abstract Iterator<ResourcePersistentId> getResourcePidIterator();
protected abstract Iterator<ResourcePersistentId> getResourcePidIterator();
protected List<SearchParameterMap> createSearchParameterMapsForResourceType() {
BulkExportJobEntity jobEntity = getJobEntity();

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportCreateEntityStepListener.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportCreateEntityStepListener.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -20,16 +20,12 @@ package ca.uhn.fhir.jpa.bulk.job;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
import org.springframework.batch.core.BatchStatus;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import org.springframework.batch.core.ExitStatus;
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.StepExecutionListener;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/**
* Will run before and after a job to set the status to whatever is appropriate.
@ -43,7 +39,7 @@ public class BulkExportCreateEntityStepListener implements StepExecutionListener
public void beforeStep(StepExecution theStepExecution) {
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString("jobUUID");
if (jobUuid != null) {
myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkJobStatusEnum.BUILDING);
myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkExportJobStatusEnum.BUILDING);
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportGenerateResourceFilesStepListener.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportGenerateResourceFilesStepListener.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.bulk.job;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import org.springframework.batch.core.ExitStatus;
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.StepExecutionListener;
@ -55,7 +55,7 @@ public class BulkExportGenerateResourceFilesStepListener implements StepExecutio
}
assert isNotBlank(jobUuid);
String exitDescription = theStepExecution.getExitStatus().getExitDescription();
myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkJobStatusEnum.ERROR, exitDescription);
myBulkExportDaoSvc.setJobToStatus(jobUuid, BulkExportJobStatusEnum.ERROR, exitDescription);
}
return theStepExecution.getExitStatus();
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportJobCloser.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobCloser.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.bulk.job;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import org.springframework.batch.core.BatchStatus;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
@ -44,9 +44,9 @@ public class BulkExportJobCloser implements Tasklet {
@Override
public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) {
if (theChunkContext.getStepContext().getStepExecution().getJobExecution().getStatus() == BatchStatus.STARTED) {
myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkJobStatusEnum.COMPLETE);
myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkExportJobStatusEnum.COMPLETE);
} else {
myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkJobStatusEnum.ERROR);
myBulkExportDaoSvc.setJobToStatus(myJobUUID, BulkExportJobStatusEnum.ERROR);
}
return RepeatStatus.FINISHED;
}

31
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportJobConfig.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobConfig.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -23,7 +23,7 @@ package ca.uhn.fhir.jpa.bulk.job;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.processors.GoldenResourceAnnotatingProcessor;
import ca.uhn.fhir.jpa.batch.processors.PidToIBaseResourceProcessor;
import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -35,8 +35,6 @@ import org.springframework.batch.core.configuration.annotation.JobScope;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.batch.item.ItemProcessor;
import org.springframework.batch.item.ItemReader;
import org.springframework.batch.item.ItemWriter;
import org.springframework.batch.item.support.CompositeItemProcessor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
@ -59,6 +57,7 @@ public class BulkExportJobConfig {
public static final String GROUP_ID_PARAMETER = "groupId";
public static final String RESOURCE_TYPES_PARAMETER = "resourceTypes";
public static final int CHUNK_SIZE = 100;
public static final String JOB_DESCRIPTION = "jobDescription";
@Autowired
private StepBuilderFactory myStepBuilderFactory;
@ -90,9 +89,9 @@ public class BulkExportJobConfig {
@Lazy
public Job bulkExportJob() {
return myJobBuilderFactory.get(BatchJobsConfig.BULK_EXPORT_JOB_NAME)
.validator(bulkJobParameterValidator())
.validator(bulkExportJobParameterValidator())
.start(createBulkExportEntityStep())
.next(partitionStep())
.next(bulkExportPartitionStep())
.next(closeJobStep())
.build();
}
@ -114,7 +113,7 @@ public class BulkExportJobConfig {
public Job groupBulkExportJob() {
return myJobBuilderFactory.get(BatchJobsConfig.GROUP_BULK_EXPORT_JOB_NAME)
.validator(groupBulkJobParameterValidator())
.validator(bulkJobParameterValidator())
.validator(bulkExportJobParameterValidator())
.start(createBulkExportEntityStep())
.next(groupPartitionStep())
.next(closeJobStep())
@ -125,7 +124,7 @@ public class BulkExportJobConfig {
@Lazy
public Job patientBulkExportJob() {
return myJobBuilderFactory.get(BatchJobsConfig.PATIENT_BULK_EXPORT_JOB_NAME)
.validator(bulkJobParameterValidator())
.validator(bulkExportJobParameterValidator())
.start(createBulkExportEntityStep())
.next(patientPartitionStep())
.next(closeJobStep())
@ -150,8 +149,9 @@ public class BulkExportJobConfig {
return new CreateBulkExportEntityTasklet();
}
@Bean
public JobParametersValidator bulkJobParameterValidator() {
public JobParametersValidator bulkExportJobParameterValidator() {
return new BulkExportJobParameterValidator();
}
@ -159,7 +159,7 @@ public class BulkExportJobConfig {
@Bean
public Step groupBulkExportGenerateResourceFilesStep() {
return myStepBuilderFactory.get("groupBulkExportGenerateResourceFilesStep")
.<List<ResourcePersistentId>, List<IBaseResource>> chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.<List<ResourcePersistentId>, List<IBaseResource>>chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.reader(groupBulkItemReader())
.processor(inflateResourceThenAnnotateWithGoldenResourceProcessor())
.writer(resourceToFileWriter())
@ -170,17 +170,18 @@ public class BulkExportJobConfig {
@Bean
public Step bulkExportGenerateResourceFilesStep() {
return myStepBuilderFactory.get("bulkExportGenerateResourceFilesStep")
.<List<ResourcePersistentId>, List<IBaseResource>> chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.<List<ResourcePersistentId>, List<IBaseResource>>chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.reader(bulkItemReader())
.processor(myPidToIBaseResourceProcessor)
.writer(resourceToFileWriter())
.listener(bulkExportGenerateResourceFilesStepListener())
.build();
}
@Bean
public Step patientBulkExportGenerateResourceFilesStep() {
return myStepBuilderFactory.get("patientBulkExportGenerateResourceFilesStep")
.<List<ResourcePersistentId>, List<IBaseResource>> chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.<List<ResourcePersistentId>, List<IBaseResource>>chunk(CHUNK_SIZE) //1000 resources per generated file, as the reader returns 10 resources at a time.
.reader(patientBulkItemReader())
.processor(myPidToIBaseResourceProcessor)
.writer(resourceToFileWriter())
@ -214,7 +215,7 @@ public class BulkExportJobConfig {
}
@Bean
public Step partitionStep() {
public Step bulkExportPartitionStep() {
return myStepBuilderFactory.get("partitionStep")
.partitioner("bulkExportGenerateResourceFilesStep", bulkExportResourceTypePartitioner())
.step(bulkExportGenerateResourceFilesStep())
@ -240,7 +241,7 @@ public class BulkExportJobConfig {
@Bean
@StepScope
public GroupBulkItemReader groupBulkItemReader(){
public GroupBulkItemReader groupBulkItemReader() {
return new GroupBulkItemReader();
}
@ -252,7 +253,7 @@ public class BulkExportJobConfig {
@Bean
@StepScope
public BulkItemReader bulkItemReader(){
public BulkItemReader bulkItemReader() {
return new BulkItemReader();
}

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportJobParameterValidator.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParameterValidator.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -24,7 +24,6 @@ import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
import ca.uhn.fhir.jpa.entity.BulkExportJobEntity;
import ca.uhn.fhir.rest.api.Constants;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.JobParametersValidator;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkExportJobParametersBuilder.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkExportJobParametersBuilder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.job;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
import ca.uhn.fhir.rest.api.Constants;
import org.springframework.batch.core.JobParametersBuilder;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/BulkItemReader.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/BulkItemReader.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -29,7 +29,6 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.slf4j.Logger;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
@ -43,7 +42,7 @@ public class BulkItemReader extends BaseBulkItemReader {
private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
@Override
Iterator<ResourcePersistentId> getResourcePidIterator() {
protected Iterator<ResourcePersistentId> getResourcePidIterator() {
ourLog.info("Bulk export assembling export of type {} for job {}", myResourceType, myJobUUID);
Set<ResourcePersistentId> myReadPids = new HashSet<>();

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/CreateBulkExportEntityTasklet.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/CreateBulkExportEntityTasklet.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -20,8 +20,8 @@ package ca.uhn.fhir.jpa.bulk.job;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.Constants;
import org.apache.commons.lang3.StringUtils;
@ -87,7 +87,7 @@ public class CreateBulkExportEntityTasklet implements Tasklet {
}
}
private void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
public static void addUUIDToJobContext(ChunkContext theChunkContext, String theJobUUID) {
theChunkContext
.getStepContext()
.getStepExecution()

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkExportJobParametersBuilder.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkExportJobParametersBuilder.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L

17
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupBulkItemReader.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupBulkItemReader.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.dao.data.IMdmLinkDao;
import ca.uhn.fhir.jpa.dao.index.IdHelperService;
import ca.uhn.fhir.jpa.dao.mdm.MdmExpansionCacheSvc;
import ca.uhn.fhir.jpa.model.search.SearchRuntimeDetails;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.util.QueryChunker;
import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
@ -36,7 +37,6 @@ import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import com.google.common.collect.Multimaps;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
@ -81,7 +81,7 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
private MdmExpansionCacheSvc myMdmExpansionCacheSvc;
@Override
Iterator<ResourcePersistentId> getResourcePidIterator() {
protected Iterator<ResourcePersistentId> getResourcePidIterator() {
Set<ResourcePersistentId> myReadPids = new HashSet<>();
//Short circuit out if we detect we are attempting to extract patients
@ -119,7 +119,8 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
Set<Long> patientPidsToExport = new HashSet<>(pidsOrThrowException);
if (myMdmEnabled) {
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
SystemRequestDetails srd = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), srd);
Long pidOrNull = myIdHelperService.getPidOrNull(group);
List<IMdmLinkDao.MdmPidTuple> goldenPidSourcePidTuple = myMdmLinkDao.expandPidsFromGroupPidGivenMatchResult(pidOrNull, MdmMatchResultEnum.MATCH);
goldenPidSourcePidTuple.forEach(tuple -> {
@ -179,13 +180,12 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
* @return A list of strings representing the Patient IDs of the members (e.g. ["P1", "P2", "P3"]
*/
private List<String> getMembers() {
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), requestDetails);
List<IPrimitiveType> evaluate = myContext.newFhirPath().evaluate(group, "member.entity.reference", IPrimitiveType.class);
return evaluate.stream().map(IPrimitiveType::getValueAsString).collect(Collectors.toList());
}
/**
* Given the local myGroupId, perform an expansion to retrieve all resource IDs of member patients.
* if myMdmEnabled is set to true, we also reach out to the IMdmLinkDao to attempt to also expand it into matched
@ -195,7 +195,8 @@ public class GroupBulkItemReader extends BaseBulkItemReader implements ItemReade
*/
private Set<String> expandAllPatientPidsFromGroup() {
Set<String> expandedIds = new HashSet<>();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId));
SystemRequestDetails requestDetails = SystemRequestDetails.newSystemRequestAllPartitions();
IBaseResource group = myDaoRegistry.getResourceDao("Group").read(new IdDt(myGroupId), requestDetails);
Long pidOrNull = myIdHelperService.getPidOrNull(group);
//Attempt to perform MDM Expansion of membership

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/GroupIdPresentValidator.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/GroupIdPresentValidator.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -26,7 +26,7 @@ import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.JobParametersValidator;
import static ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig.*;
import static ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig.*;
import static org.slf4j.LoggerFactory.getLogger;
public class GroupIdPresentValidator implements JobParametersValidator {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/PatientBulkItemReader.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/PatientBulkItemReader.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -61,7 +61,7 @@ public class PatientBulkItemReader extends BaseBulkItemReader implements ItemRea
}
@Override
Iterator<ResourcePersistentId> getResourcePidIterator() {
protected Iterator<ResourcePersistentId> getResourcePidIterator() {
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
String errorMessage = "You attempted to start a Patient Bulk Export, but the system has `Index Missing Fields` disabled. It must be enabled for Patient Bulk Export";
ourLog.error(errorMessage);

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceToFileWriter.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceToFileWriter.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -25,8 +25,9 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.DaoMethodOutcome;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.entity.BulkExportCollectionFileEntity;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.util.BinaryUtil;
@ -100,7 +101,7 @@ public class ResourceToFileWriter implements ItemWriter<List<IBaseResource>> {
IBaseBinary binary = BinaryUtil.newBinary(myFhirContext);
binary.setContentType(Constants.CT_FHIR_NDJSON);
binary.setContent(myOutputStream.toByteArray());
DaoMethodOutcome outcome = myBinaryDao.create(binary);
DaoMethodOutcome outcome = myBinaryDao.create(binary, new SystemRequestDetails());
return outcome.getResource().getIdElement();
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/job/ResourceTypePartitioner.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/job/ResourceTypePartitioner.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.job;
package ca.uhn.fhir.jpa.bulk.export.job;
/*-
* #%L
@ -20,7 +20,7 @@ package ca.uhn.fhir.jpa.bulk.job;
* #L%
*/
import ca.uhn.fhir.jpa.bulk.svc.BulkExportDaoSvc;
import ca.uhn.fhir.jpa.bulk.export.svc.BulkExportDaoSvc;
import org.slf4j.Logger;
import org.springframework.batch.core.partition.support.Partitioner;
import org.springframework.batch.item.ExecutionContext;

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/model/BulkJobStatusEnum.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/model/BulkExportJobStatusEnum.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.model;
package ca.uhn.fhir.jpa.bulk.export.model;
/*-
* #%L
@ -20,7 +20,14 @@ package ca.uhn.fhir.jpa.bulk.model;
* #L%
*/
public enum BulkJobStatusEnum {
import com.fasterxml.jackson.annotation.JsonFormat;
@JsonFormat(shape = JsonFormat.Shape.STRING)
public enum BulkExportJobStatusEnum {
/**
* Sorting OK!
*/
SUBMITTED,
BUILDING,

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/model/BulkExportResponseJson.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/model/BulkExportResponseJson.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.model;
package ca.uhn.fhir.jpa.bulk.export.model;
/*-
* #%L

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/provider/BulkDataExportProvider.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/provider/BulkDataExportProvider.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.provider;
package ca.uhn.fhir.jpa.bulk.export.provider;
/*-
* #%L
@ -21,9 +21,9 @@ package ca.uhn.fhir.jpa.bulk.provider;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportResponseJson;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;

36
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/svc/BulkDataExportSvcImpl.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkDataExportSvcImpl.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.svc;
package ca.uhn.fhir.jpa.bulk.export.svc;
/*-
* #%L
@ -23,16 +23,15 @@ package ca.uhn.fhir.jpa.bulk.svc;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.fhirpath.IFhirPath;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.batch.BatchJobsConfig;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions;
import ca.uhn.fhir.jpa.bulk.export.api.IBulkDataExportSvc;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
@ -43,16 +42,13 @@ import ca.uhn.fhir.jpa.model.sched.HapiJob;
import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.InstantType;
import org.quartz.JobExecutionContext;
@ -78,9 +74,9 @@ import java.util.Set;
import java.util.UUID;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions.ExportStyle.GROUP;
import static ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions.ExportStyle.PATIENT;
import static ca.uhn.fhir.jpa.bulk.api.BulkDataExportOptions.ExportStyle.SYSTEM;
import static ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions.ExportStyle.GROUP;
import static ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions.ExportStyle.PATIENT;
import static ca.uhn.fhir.jpa.bulk.export.api.BulkDataExportOptions.ExportStyle.SYSTEM;
import static ca.uhn.fhir.util.UrlUtil.escapeUrlParam;
import static ca.uhn.fhir.util.UrlUtil.escapeUrlParams;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
@ -136,7 +132,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
Optional<BulkExportJobEntity> jobToProcessOpt = myTxTemplate.execute(t -> {
Pageable page = PageRequest.of(0, 1);
Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByStatus(page, BulkJobStatusEnum.SUBMITTED);
Slice<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByStatus(page, BulkExportJobStatusEnum.SUBMITTED);
if (submittedJobs.isEmpty()) {
return Optional.empty();
}
@ -158,7 +154,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
Optional<BulkExportJobEntity> submittedJobs = myBulkExportJobDao.findByJobId(jobUuid);
if (submittedJobs.isPresent()) {
BulkExportJobEntity jobEntity = submittedJobs.get();
jobEntity.setStatus(BulkJobStatusEnum.ERROR);
jobEntity.setStatus(BulkExportJobStatusEnum.ERROR);
jobEntity.setStatusMessage(e.getMessage());
myBulkExportJobDao.save(jobEntity);
}
@ -208,8 +204,8 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
ourLog.info("Purging bulk data file: {}", nextFile.getResourceId());
getBinaryDao().delete(toId(nextFile.getResourceId()));
getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), null);
getBinaryDao().delete(toId(nextFile.getResourceId()), new SystemRequestDetails());
getBinaryDao().forceExpungeInExistingTransaction(toId(nextFile.getResourceId()), new ExpungeOptions().setExpungeDeletedResources(true).setExpungeOldVersions(true), new SystemRequestDetails());
myBulkExportCollectionFileDao.deleteByPid(nextFile.getId());
}
@ -344,7 +340,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
if (useCache) {
Date cutoff = DateUtils.addMilliseconds(new Date(), -myReuseBulkExportForMillis);
Pageable page = PageRequest.of(0, 10);
Slice<BulkExportJobEntity> existing = myBulkExportJobDao.findExistingJob(page, request, cutoff, BulkJobStatusEnum.ERROR);
Slice<BulkExportJobEntity> existing = myBulkExportJobDao.findExistingJob(page, request, cutoff, BulkExportJobStatusEnum.ERROR);
if (!existing.isEmpty()) {
return toSubmittedJobInfo(existing.iterator().next());
}
@ -373,7 +369,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
BulkExportJobEntity job = new BulkExportJobEntity();
job.setJobId(UUID.randomUUID().toString());
job.setStatus(BulkJobStatusEnum.SUBMITTED);
job.setStatus(BulkExportJobStatusEnum.SUBMITTED);
job.setSince(since);
job.setCreated(new Date());
job.setRequest(request);
@ -445,7 +441,7 @@ public class BulkDataExportSvcImpl implements IBulkDataExportSvc {
retVal.setStatusMessage(job.getStatusMessage());
retVal.setRequest(job.getRequest());
if (job.getStatus() == BulkJobStatusEnum.COMPLETE) {
if (job.getStatus() == BulkExportJobStatusEnum.COMPLETE) {
for (BulkExportCollectionEntity nextCollection : job.getCollections()) {
for (BulkExportCollectionFileEntity nextFile : nextCollection.getFiles()) {
retVal.addFile()

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/svc/BulkExportCollectionFileDaoSvc.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkExportCollectionFileDaoSvc.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.svc;
package ca.uhn.fhir.jpa.bulk.export.svc;
/*-
* #%L

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/svc/BulkExportDaoSvc.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/export/svc/BulkExportDaoSvc.java
View File

@ -1,4 +1,4 @@
package ca.uhn.fhir.jpa.bulk.svc;
package ca.uhn.fhir.jpa.bulk.export.svc;
/*-
* #%L
@ -20,9 +20,7 @@ package ca.uhn.fhir.jpa.bulk.svc;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.bulk.model.BulkJobStatusEnum;
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportCollectionFileDao;
import ca.uhn.fhir.jpa.dao.data.IBulkExportJobDao;
@ -84,12 +82,12 @@ public class BulkExportDaoSvc {
}
@Transactional
public void setJobToStatus(String theJobUUID, BulkJobStatusEnum theStatus) {
public void setJobToStatus(String theJobUUID, BulkExportJobStatusEnum theStatus) {
setJobToStatus(theJobUUID, theStatus, null);
}
@Transactional
public void setJobToStatus(String theJobUUID, BulkJobStatusEnum theStatus, String theStatusMessage) {
public void setJobToStatus(String theJobUUID, BulkExportJobStatusEnum theStatus, String theStatusMessage) {
Optional<BulkExportJobEntity> oJob = myBulkExportJobDao.findByJobId(theJobUUID);
if (!oJob.isPresent()) {
ourLog.error("Job with UUID {} doesn't exist!", theJobUUID);

93
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/api/IBulkDataImportSvc.java Normal file
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@ -0,0 +1,93 @@
package ca.uhn.fhir.jpa.bulk.imprt.api;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobJson;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
import javax.annotation.Nonnull;
import java.util.List;
public interface IBulkDataImportSvc {
/**
* Create a new job in {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#STAGING STAGING} state (meaning it won't yet be worked on and can be added to)
*/
String createNewJob(BulkImportJobJson theJobDescription, @Nonnull List<BulkImportJobFileJson> theInitialFiles);
/**
* Add more files to a job in {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#STAGING STAGING} state
*
* @param theJobId The job ID
* @param theFiles The files to add to the job
*/
void addFilesToJob(String theJobId, List<BulkImportJobFileJson> theFiles);
/**
* Move a job from {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#STAGING STAGING}
* state to {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#READY READY}
* state, meaning that is is a candidate to be picked up for processing
*
* @param theJobId The job ID
*/
void markJobAsReadyForActivation(String theJobId);
/**
* This method is intended to be called from the job scheduler, and will begin execution on
* the next job in status {@link ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum#READY READY}
*
* @return Returns {@literal true} if a job was activated
*/
boolean activateNextReadyJob();
/**
* Updates the job status for the given job
*/
void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus);
/**
* Updates the job status for the given job
*/
void setJobToStatus(String theJobId, BulkImportJobStatusEnum theStatus, String theStatusMessage);
/**
* Gets the number of files available for a given Job ID
*
* @param theJobId The job ID
* @return The file count
*/
BulkImportJobJson fetchJob(String theJobId);
/**
* Fetch a given file by job ID
*
* @param theJobId The job ID
* @param theFileIndex The index of the file within the job
* @return The file
*/
BulkImportJobFileJson fetchFile(String theJobId, int theFileIndex);
/**
* Delete all input files associated with a particular job
*/
void deleteJobFiles(String theJobId);
}

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/ActivateBulkImportEntityStepListener.java Normal file
View File

@ -0,0 +1,51 @@
package ca.uhn.fhir.jpa.bulk.imprt.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
import org.springframework.batch.core.ExitStatus;
import org.springframework.batch.core.StepExecution;
import org.springframework.batch.core.StepExecutionListener;
import org.springframework.beans.factory.annotation.Autowired;
/**
* Will run before and after a job to set the status to whatever is appropriate.
*/
public class ActivateBulkImportEntityStepListener implements StepExecutionListener {
@Autowired
private IBulkDataImportSvc myBulkImportDaoSvc;
@Override
public void beforeStep(StepExecution theStepExecution) {
String jobUuid = theStepExecution.getJobExecution().getJobParameters().getString(BulkExportJobConfig.JOB_UUID_PARAMETER);
if (jobUuid != null) {
myBulkImportDaoSvc.setJobToStatus(jobUuid, BulkImportJobStatusEnum.RUNNING);
}
}
@Override
public ExitStatus afterStep(StepExecution theStepExecution) {
return ExitStatus.EXECUTING;
}
}

76
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileReader.java Normal file
View File

@ -0,0 +1,76 @@
package ca.uhn.fhir.jpa.bulk.imprt.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.batch.log.Logs;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobFileJson;
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
import ca.uhn.fhir.util.IoUtil;
import com.google.common.io.LineReader;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.batch.item.ItemReader;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import java.io.StringReader;
@SuppressWarnings("UnstableApiUsage")
public class BulkImportFileReader implements ItemReader<ParsedBulkImportRecord> {
@Autowired
private IBulkDataImportSvc myBulkDataImportSvc;
@Autowired
private FhirContext myFhirContext;
@Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
private String myJobUuid;
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
private int myFileIndex;
private StringReader myReader;
private LineReader myLineReader;
private int myLineIndex;
private String myTenantName;
@Override
public ParsedBulkImportRecord read() throws Exception {
if (myReader == null) {
BulkImportJobFileJson file = myBulkDataImportSvc.fetchFile(myJobUuid, myFileIndex);
myTenantName = file.getTenantName();
myReader = new StringReader(file.getContents());
myLineReader = new LineReader(myReader);
}
String nextLine = myLineReader.readLine();
if (nextLine == null) {
IoUtil.closeQuietly(myReader);
return null;
}
Logs.getBatchTroubleshootingLog().debug("Reading line {} file index {} for job: {}", myLineIndex++, myFileIndex, myJobUuid);
IBaseResource parsed = myFhirContext.newJsonParser().parseResource(nextLine);
return new ParsedBulkImportRecord(myTenantName, parsed);
}
}

74
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportFileWriter.java Normal file
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@ -0,0 +1,74 @@
package ca.uhn.fhir.jpa.bulk.imprt.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.model.JobFileRowProcessingModeEnum;
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import java.util.List;
public class BulkImportFileWriter implements ItemWriter<ParsedBulkImportRecord> {
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportFileWriter.class);
@Value("#{stepExecutionContext['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
private String myJobUuid;
@Value("#{stepExecutionContext['" + BulkImportPartitioner.FILE_INDEX + "']}")
private int myFileIndex;
@Value("#{stepExecutionContext['" + BulkImportPartitioner.ROW_PROCESSING_MODE + "']}")
private JobFileRowProcessingModeEnum myRowProcessingMode;
@Autowired
private DaoRegistry myDaoRegistry;
@SuppressWarnings({"SwitchStatementWithTooFewBranches", "rawtypes", "unchecked"})
@Override
public void write(List<? extends ParsedBulkImportRecord> theItemLists) throws Exception {
ourLog.info("Beginning bulk import write {} chunks Job[{}] FileIndex[{}]", theItemLists.size(), myJobUuid, myFileIndex);
for (ParsedBulkImportRecord nextItem : theItemLists) {
SystemRequestDetails requestDetails = new SystemRequestDetails();
requestDetails.setTenantId(nextItem.getTenantName());
// Yeah this is a lame switch - We'll add more later I swear
switch (myRowProcessingMode) {
default:
case FHIR_TRANSACTION:
IFhirSystemDao systemDao = myDaoRegistry.getSystemDao();
IBaseResource inputBundle = nextItem.getRowContent();
systemDao.transactionNested(requestDetails, inputBundle);
break;
}
}
}
}

57
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobCloser.java Normal file
View File

@ -0,0 +1,57 @@
package ca.uhn.fhir.jpa.bulk.imprt.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.bulk.export.job.BulkExportJobConfig;
import ca.uhn.fhir.jpa.bulk.imprt.api.IBulkDataImportSvc;
import ca.uhn.fhir.jpa.bulk.imprt.model.BulkImportJobStatusEnum;
import org.springframework.batch.core.BatchStatus;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
/**
* Will run before and after a job to set the status to whatever is appropriate.
*/
public class BulkImportJobCloser implements Tasklet {
@Value("#{jobParameters['" + BulkExportJobConfig.JOB_UUID_PARAMETER + "']}")
private String myJobUUID;
@Autowired
private IBulkDataImportSvc myBulkDataImportSvc;
@Override
public RepeatStatus execute(StepContribution theStepContribution, ChunkContext theChunkContext) {
BatchStatus executionStatus = theChunkContext.getStepContext().getStepExecution().getJobExecution().getStatus();
if (executionStatus == BatchStatus.STARTED) {
myBulkDataImportSvc.setJobToStatus(myJobUUID, BulkImportJobStatusEnum.COMPLETE);
myBulkDataImportSvc.deleteJobFiles(myJobUUID);
} else {
myBulkDataImportSvc.setJobToStatus(myJobUUID, BulkImportJobStatusEnum.ERROR, "Found job in status: " + executionStatus);
myBulkDataImportSvc.deleteJobFiles(myJobUUID);
}
return RepeatStatus.FINISHED;
}
}

169
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/bulk/imprt/job/BulkImportJobConfig.java Normal file
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@ -0,0 +1,169 @@
package ca.uhn.fhir.jpa.bulk.imprt.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.batch.BatchConstants;
import ca.uhn.fhir.jpa.bulk.imprt.model.ParsedBulkImportRecord;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobParametersValidator;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.JobScope;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.batch.core.partition.PartitionHandler;
import org.springframework.batch.core.partition.support.TaskExecutorPartitionHandler;
import org.springframework.batch.item.ItemWriter;
import org.springframework.batch.repeat.CompletionPolicy;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.core.task.TaskExecutor;
import static ca.uhn.fhir.jpa.batch.BatchJobsConfig.BULK_IMPORT_JOB_NAME;
/**
* Spring batch Job configuration file. Contains all necessary plumbing to run a
* Bulk Export job.
*/
@Configuration
public class BulkImportJobConfig {
public static final String JOB_PARAM_COMMIT_INTERVAL = "commitInterval";
@Autowired
private StepBuilderFactory myStepBuilderFactory;
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Autowired
@Qualifier(BatchConstants.JOB_LAUNCHING_TASK_EXECUTOR)
private TaskExecutor myTaskExecutor;
@Bean(name = BULK_IMPORT_JOB_NAME)
@Lazy
public Job bulkImportJob() throws Exception {
return myJobBuilderFactory.get(BULK_IMPORT_JOB_NAME)
.validator(bulkImportJobParameterValidator())
.start(bulkImportPartitionStep())
.next(bulkImportCloseJobStep())
.build();
}
@Bean
public JobParametersValidator bulkImportJobParameterValidator() {
return new BulkImportJobParameterValidator();
}
@Bean
public CreateBulkImportEntityTasklet createBulkImportEntityTasklet() {
return new CreateBulkImportEntityTasklet();
}
@Bean
@JobScope
public ActivateBulkImportEntityStepListener activateBulkImportEntityStepListener() {
return new ActivateBulkImportEntityStepListener();
}
@Bean
public Step bulkImportPartitionStep() throws Exception {
return myStepBuilderFactory.get("bulkImportPartitionStep")
.partitioner("bulkImportPartitionStep", bulkImportPartitioner())
.partitionHandler(partitionHandler())
.listener(activateBulkImportEntityStepListener())
.gridSize(10)
.build();
}
private PartitionHandler partitionHandler() throws Exception {
assert myTaskExecutor != null;
TaskExecutorPartitionHandler retVal = new TaskExecutorPartitionHandler();
retVal.setStep(bulkImportProcessFilesStep());
retVal.setTaskExecutor(myTaskExecutor);
retVal.afterPropertiesSet();
return retVal;
}
@Bean
public Step bulkImportCloseJobStep() {
return myStepBuilderFactory.get("bulkImportCloseJobStep")
.tasklet(bulkImportJobCloser())
.build();
}
@Bean
@JobScope
public BulkImportJobCloser bulkImportJobCloser() {
return new BulkImportJobCloser();
}
@Bean
@JobScope
public BulkImportPartitioner bulkImportPartitioner() {
return new BulkImportPartitioner();
}
@Bean
public Step bulkImportProcessFilesStep() {
CompletionPolicy completionPolicy = completionPolicy();
return myStepBuilderFactory.get("bulkImportProcessFilesStep")
.<ParsedBulkImportRecord, ParsedBulkImportRecord>chunk(completionPolicy)
.reader(bulkImportFileReader())
.writer(bulkImportFileWriter())
.listener(bulkImportStepListener())
.listener(completionPolicy)
.build();
}
@Bean
@StepScope
public CompletionPolicy completionPolicy() {
return new BulkImportProcessStepCompletionPolicy();
}
@Bean
@StepScope
public ItemWriter<ParsedBulkImportRecord> bulkImportFileWriter() {
return new BulkImportFileWriter();
}
@Bean
@StepScope
public BulkImportFileReader bulkImportFileReader() {
return new BulkImportFileReader();
}
@Bean
@StepScope
public BulkImportStepListener bulkImportStepListener() {
return new BulkImportStepListener();
}
}

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